I've never liked the automatic conversion in Beer Smith, so I've worked out a procedure I use when converting a big all-grain recipe to my partial boil partial mash system. As an example, I'm using Mr Wort's excellent Rye IPA recipe.
First, I load up the entire recipe as it is, matching the batch and boil volumes and adjust efficiency so the OG matches what's listed in the recipe.
I make note of the OG, Color and IBU stats for the recipe, then I adjust the batch size to what my boil size will be and reduce the amount of base malt until the OG is the same as it was to start with.
At that point, I put the batch size back to the original number, and lower the boil volume to my number (the same as I used for batch size a moment ago).
Next, I add some extract. In this case I used extra light DME. You want to add enough extract to bring the OG back up to where it should be according to the recipe. You want to specify that the extract will be "added after the boil", so you'll add the extract at the end and heat the wort just long enough to get it incorporated.
You'll notice the color is still the same as I had for the original recipe. That is because I'm boiling the same density of liquid as I would with a full boil of the original recipe. The IBU's are a little lower, but if you want them to matchexactly, it's just a minor adjustment. In this case, a quarter ounce of hops.
I like this method because I can keep the specialty grains the same as the original recipe and keep the hops as close to the same as possible, because I'm not changing the concentration of wort in the boil.
I use a 5-gallon igloo beverage cooler for my partial mash, so I'm able to do quite a bit of grain. Folks mashing in their spaghetti pot might not be able to do this with all recipes since some convert to larger grain bills than others.